NucPred on Proteomes

Authors: Andrea Krings, Amine Heddad, Markus Brameier and Bob MacCallum, Stockholm Bioinformatics Center, Stockholm University, Sweden.

NucPred - predictions for eukaryotic proteomes

Species:

Note: All filters/tests are combined with AND unless otherwise stated

Show only the proteins with links to database(s):
OMIM - human disease genes
PDB - protein 3D structure
( AND OR combination )

Annotation filters (can be slow! - Perl regexps allowed: e.g. nucleus|nucleolus)

UniProt ID (e.g. "PK3B_")
UniProt description (e.g. "kinase")
UniProt subcellular location
AND
UniProt GO component
AND
AND the
AND the

Only show proteins where the PredictNLS prediction is:

positive
negative

Only show proteins where the PSORT II predicted location

is is not

Click here: to filter by NucPred score

exclude all transmembrane proteins predicted by TMHMM
don't exclude lone N-terminal predicted transmembrane helices
(these could be signal peptides)

export all ACs and IDs as text file

Show proteins (ordered by NucPred score ) from to (currently 98716 matches)

You can bookmark/save your search criteria with this link. You can also start again with default settings.

UniProt accession	UniProt ID	UniProt description	NucPred score	Predict- NLS	PSORT II	TMHMM #helices	UniProt annotation for subcellular location	Uniprot GO cellular component	OMIM	PDB	sequence length
Q9BXF6 UniProt NPD GO	RFIP5_HUMAN	Rab11 family-interacting protein 5 (Rab11-FIP5) (Rab11-interacting protein Rip11) (Gamma-SNAP-associ ...	0.68	-	nuc	0	Cytoplasm. Endosome; recycling endosome; recycling endosomal membrane; peripheral membrane protein. ...	mitochondrial outer membrane [IDA]	605536		653
Q9JM13 UniProt NPD GO	RABX5_MOUSE	Rab5 GDP/GTP exchange factor (Rabex-5)	0.68	-	nuc	0	Cytoplasm (By similarity). Endosome; early endosome (By similarity). Endosome; recycling endosome (B ...				491
P46695 UniProt NPD GO	IEX1_HUMAN	Radiation-inducible immediate-early gene IEX-1 (Immediate early protein GLY96) (Immediate early resp ...	0.68	-	nuc	0	Membrane; single-pass type II membrane protein (Potential)		602996		156
Q68DN6 UniProt NPD GO	RBP26_HUMAN	Ran-binding protein 2-like 6 (RanBP2L6)	0.68	-	nuc	0					1748
Q64487 UniProt NPD GO	PTPRD_MOUSE	Receptor-type tyrosine-protein phosphatase delta precursor (EC 3.1.3.48) (Protein-tyrosine phosphata ...	0.68	+	nuc	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [ISS]			1894
Q9UGC6 UniProt NPD GO	RGS17_HUMAN	Regulator of G-protein signaling 17 (RGS17)	0.68	-	mit	0	Membrane; lipid-anchor (Potential)		607191	1ZV4	210
Q9NS28 UniProt NPD GO	RGS18_HUMAN	Regulator of G-protein signaling 18 (RGS18)	0.68	-	nuc	0	Cytoplasm (By similarity)		607192		235
Q8C0D4 UniProt NPD GO	RHG12_MOUSE	Rho-GTPase-activating protein 12	0.68	-	nuc	0					838
P35688 UniProt NPD GO	LRG1_YEAST	Rho-GTPase-activating protein LRG1 (LIM-RhoGAP protein 1)	0.68	-	nuc	0	Cytoplasm. Bud. Bud neck. Localized to the bud site during bud formation and at the bud neck during ...	bud neck [IDA] cytoplasm [IDA] mitochondrion [IDA]			1017
Q8VD86 UniProt NPD GO	RNS1D_RATRT	Ribonuclease pancreatic delta-type precursor (EC 3.1.27.5) (RNase 1 delta)	0.68	-	exc	0	Secreted protein (By similarity)				150
Q7TSI3 UniProt NPD GO	SAPS1_MOUSE	SAPS domain family member 1	0.68	-	nuc	0					856
Q2PC93 UniProt NPD GO	SSPO_CHICK	SCO-spondin precursor	0.68	-	nuc	0	Secreted protein; extracellular space (By similarity)				5255
O60239 UniProt NPD GO	3BP5_HUMAN	SH3 domain-binding protein 5 (SH3 domain-binding protein that preferentially associates with BTK)	0.68	-	nuc	0	Mitochondrion	cytoplasm [TAS]	605612		425
Q99961 UniProt NPD GO	SH3G1_HUMAN	SH3-containing GRB2-like protein 1 (SH3 domain protein 2B) (Extra eleven-nineteen leukemia fusion ge ...	0.68	+	nuc	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity). Associated with in ...		601768		368
O35964 UniProt NPD GO	SH3G1_RAT	SH3-containing GRB2-like protein 1 (SH3 domain protein 2B) (SH3p8)	0.68	+	nuc	0	Cytoplasm. Membrane; peripheral membrane protein. Associated with internal membranes. Concentrated i ...				368
Q4WRE2 UniProt NPD GO	SWC5_ASPFU	SWR1-complex protein 5	0.68	+	nuc	0	Nucleus (By similarity)				359
P20616 UniProt NPD GO	SCG2_BOVIN	Secretogranin-2 precursor (Secretogranin II) (SgII) (Chromogranin C) [Contains: Secretoneurin (SN)]	0.68	-	exc	0	Neuroendocrine and endocrine secretory granules	extracellular space [ISS]			613
P10362 UniProt NPD GO	SCG2_RAT	Secretogranin-2 precursor (Secretogranin II) (SgII) (Chromogranin C) [Contains: Secretoneurin (SN)]	0.68	-	exc	1 *	Neuroendocrine and endocrine secretory granules	extracellular space [ISS] secretory granule [TAS]			619
Q9WUH7 UniProt NPD GO	SEM4G_MOUSE	Semaphorin-4G precursor	0.68	-	exc	1	Membrane; single-pass type I membrane protein				837
Q5U7M8 UniProt NPD GO	SEMG2_COLGU	Semenogelin-2 precursor (Semenogelin II) (SGII)	0.68	-	nuc	0	Secreted protein (By similarity)				582
Q5A649 UniProt NPD GO	ATG1_CANAL	Serine/threonine-protein kinase ATG1 (EC 2.7.11.1) (Autophagy-related protein 1)	0.68	-	nuc	0	Cytoplasm (By similarity)				834
Q75D46 UniProt NPD GO	BUR1_ASHGO	Serine/threonine-protein kinase BUR1 (EC 2.7.11.22) (EC 2.7.11.23)	0.68	-	nuc	0	Nucleus (By similarity)				753
O95810 UniProt NPD GO	SDPR_HUMAN	Serum deprivation-response protein (Phosphatidylserine-binding protein) (PS-p68)	0.68	-	nuc	0	Cytoplasm; cytosol. Colocalizes with CAV1 to caveolae	cytosol [IDA]	606728		424
Q9TUZ0 UniProt NPD GO	STA5B_PIG	Signal transducer and activator of transcription 5B	0.68	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). Translocated into the nucleus in response to pho ...				787
O88457 UniProt NPD GO	SC11A_RAT	Sodium channel protein type 11 subunit alpha (Sodium channel protein type XI subunit alpha) (Voltage ...	0.68	-	end	23	Membrane; multi-pass membrane protein (By similarity)				1765
Q2TBW7 UniProt NPD GO	SNX2_BOVIN	Sorting nexin-2	0.68	-	nuc	0					519
Q9CWK8 UniProt NPD GO	SNX2_MOUSE	Sorting nexin-2	0.68	-	nuc	0					519
Q8R496 UniProt NPD GO	SPDYA_RAT	Speedy protein A (Speedy-1) (Spy1) (Rapid inducer of G2/M progression in oocytes A) (RINGO A) (GS4)	0.68	-	nuc	0	Nucleus (By similarity)	nucleus [ISS]			312
Q9QYL0 UniProt NPD GO	HILS1_MOUSE	Spermatid-specific linker histone H1-like protein (TISP64)	0.68	-	nuc	0	Nucleus				170
P38863 UniProt NPD GO	SPC97_YEAST	Spindle pole body component SPC97	0.68	-	cyt	0	Nucleus	gamma-tubulin complex (sensu Saccharomyces) [IPI] inner plaque of spindle pole body [IDA] outer plaque of spindle pole body [IDA]			823
Q7Z698 UniProt NPD GO	SPRE2_HUMAN	Sprouty-related, EVH1 domain-containing protein 2 (Spred-2)	0.68	-	nuc	0	Membrane; peripheral membrane protein (By similarity)				418
P52823 UniProt NPD GO	STC1_HUMAN	Stanniocalcin-1 precursor (STC-1)	0.68	-	exc	0	Secreted protein		601185		247
P97574 UniProt NPD GO	STC1_RAT	Stanniocalcin-1 precursor (STC-1)	0.68	-	exc	0	Secreted protein				247
Q6BN88 UniProt NPD GO	ATG26_DEBHA	Sterol 3-beta-glucosyltransferase (EC 2.4.1.173) (Autophagy-related protein 26)	0.68	+	nuc	0	Membrane; peripheral membrane protein (Potential)				1574
Q8WXE9 UniProt NPD GO	STON2_HUMAN	Stonin-2 (Stoned B)	0.68	-	nuc	0	Cytoplasm. Membrane. Some fraction is membrane-associated		608467		905
P47169 UniProt NPD GO	ECM17_YEAST	Sulfite reductase [NADPH] subunit beta (EC 1.8.1.2) (Extracellular matrix protein 17)	0.68	+	cyt	0	Cytoplasm	cytoplasm [IDA] sulfite reductase complex (NADPH) [IDA]			1442
O18870 UniProt NPD GO	SMN_BOVIN	Survival motor neuron protein	0.68	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). Localized in subnuclear structures next to coile ...				287
Q9W6S8 UniProt NPD GO	SMN1_BRARE	Survival motor neuron protein 1	0.68	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). Localized in subnuclear structures next to coile ...				281
Q9D2G5 UniProt NPD GO	SYNJ2_MOUSE	Synaptojanin-2 (EC 3.1.3.36) (Synaptic inositol-1,4,5-trisphosphate 5-phosphatase 2)	0.68	-	mit	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity)				1434
Q9W358 UniProt NPD GO	RIC8_DROME	Synembryn (Protein Ric-8)	0.68	-	nuc	0	Cytoplasm; cell cortex. Localizes to the cell cortex	cytoplasm [IDA] cytosol [IDA]			573
O15079 UniProt NPD GO	SNPH_HUMAN	Syntaphilin	0.68	-	nuc	0	Membrane; single-pass membrane protein		604942		538
O94651 UniProt NPD GO	PEP12_SCHPO	Syntaxin pep12	0.68	-	nuc	0					317
Q86Y82 UniProt NPD GO	STX12_HUMAN	Syntaxin-12	0.68	-	nuc	1	Membrane; single-pass membrane protein (Potential)				276
Q5RBW6 UniProt NPD GO	STX12_PONPY	Syntaxin-12	0.68	-	nuc	1	Membrane; single-pass membrane protein (Potential)				276
Q8L899 UniProt NPD GO	BRI1_LYCPE	Systemin receptor SR160 precursor (EC 2.7.11.1) (Brassinosteroid LRR receptor kinase)	0.68	+	nuc	2 *	Cell membrane; single-pass type I membrane protein				1207
Q22289 UniProt NPD GO	TBX9_CAEEL	T-box transcription factor tbx-9	0.68	+	nuc	0	Nucleus	nucleus [IEP]			292
O01409 UniProt NPD GO	BRC2_HALRO	T-box-containing protein 2 (AS-T2)	0.68	-	nuc	0	Nucleus (Potential)				681
O43763 UniProt NPD GO	TLX2_HUMAN	T-cell leukemia homeobox protein 2 (Homeobox protein Hox-11L1) (Neural crest homeobox protein)	0.68	+	nuc	0	Nucleus (Probable)		604240		284
P14233 UniProt NPD GO	TGA1B_TOBAC	TGACG-sequence-specific DNA-binding protein TGA-1B (TGA1b) (HSBF) (Fragment)	0.68	-	nuc	0	Nucleus				242
Q9UIF3 UniProt NPD GO	TEKT2_HUMAN	Tektin-2 (Testicular tektin) (Tektin-t) (Testicular tektin B1-like protein) (Tektin-B1) (TEKTB1)	0.68	-	nuc	0	In sperm, observed in a discontinuous punctate pattern in the flagellum and in the postacrosomal hea ...		608953		430

You are viewing entries 14951 to 15000 of 98716. You can see more proteins by changing the limits in the form at the top of this page, or click here for the next page of proteins .

If you find NucPred useful, please cite this paper:

NucPred - Predicting Nuclear Localization of Proteins. Brameier M, Krings A, Maccallum RM. Bioinformatics, 2007. PubMed id: 17332022

The authors also look forward to your comments and suggestions.

What does the NucPred score mean?

You have to decide on a NucPred score threshold. Sequences which score greater than or equal to this threshold are predicted to spend some time in the nucleus. Higher thresholds yield fewer predicted nuclear proteins, but these predictions are more accurate (you can have higher confidence in them). The table below gives more details of the performance of NucPred estimated using the sequences it was trained on (by cross-validation). Another benchmark is available in the Bioinformatics 2007 paper.

NucPred score threshold	Specificity	Sensitivity
see above	fraction of proteins predicted to be nuclear that actually are nuclear	fraction of true nuclear proteins that are predicted (coverage)
0.10	0.45	0.88
0.20	0.52	0.83
0.30	0.57	0.77
0.40	0.63	0.69
0.50	0.70	0.62
0.60	0.71	0.53
0.70	0.81	0.44
0.80	0.84	0.32
0.90	0.88	0.21
1.00	1.00	0.02

Sequences which score >= 0.8 with NucPred and which are predicted by PredictNLS to contain an NLS have been shown to be 93% correct with a coverage of 16%. (PredictNLS by itself is 87% correct with 26% coverage on the same data.)

Go back to the NucPred Home Page.